chr12:129299385:G>A Detail (hg19) (SLC15A4)

Information

Genome

Assembly Position
hg19 chr12:129,299,385-129,299,385
hg38 chr12:128,814,840-128,814,840 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_145648.3:c.777C>T NP_663623.1:p.Asp259=
Ensemble ENST00000266771.10:c.777C>T ENST00000266771.10:p.Asp259=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.154
ToMMo:0.158
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.191

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 615806 OMIM
HGNC 23090 HGNC
Ensembl ENSG00000139370 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv47724538 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.250 Lupus Erythematosus, Systemic Significant associations were found for the single nucleotide polymorphism rs100... BeFree 20516000 Detail
0.246 Lupus Erythematosus, Systemic Significant associations were found for the single nucleotide polymorphism rs100... BeFree 20516000 Detail
Annotation

Annotations

DescrptionSourceLinks
Significant associations were found for the single nucleotide polymorphism rs10036748 of TNIP1 with ... DisGeNET Detail
Significant associations were found for the single nucleotide polymorphism rs10036748 of TNIP1 with ... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg19
Position
chr12:129,299,385-129,299,385
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1204
Mean of sample read depth (HGVD)
47.58
Standard deviation of sample read depth (HGVD)
30.23
Number of reference allele (HGVD)
2036
Number of alternative allele (HGVD)
372
Allele Frequency (HGVD)
0.15448504983388706
Gene Symbol (HGVD)
SLC15A4
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs10847697
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1583
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2653
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
1653
East Asian Heterozygous Counts (ExAC)
1337
East Asian Homozygous Counts (ExAC)
158
East Asian Allele Frequency (ExAC)
0.19114246068455135
Chromosome Counts in All Race (ExAC)
121388
Allele Counts in All Race (ExAC)
14915
Heterozygous Counts in All Race (ExAC)
12619
Homozygous Counts in All Race (ExAC)
1148
Allele Frequency in All Race (ExAC)
0.12287046495534978
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